There is a continuing need to clamp various substrates, such as silicon wafers, gallium arsenide wafers and other substrates, using a vacuum chuck while maintaining a substantially flat substrate surface. A flat substrate surface is important in microelectronics fabrication processes such as wafer fusion bonding. In the case of wafers, a flat wafer surface allows proper alignment of wafer features so that aligned fusion wafer bonding for wafer-level packaging and 3D integration can occur with a second wafer. Variations in the height of embossments on a vacuum chuck surface can lead to irregular wafer surfaces for the clamped wafer which can then lead to misalignment during a wafer bonding process. To address these variations, lapping has been used to flatten the base substrate surface of the vacuum chuck that underlies the embossments. However, this has not adequately addressed the need for improved alignment as semiconductor device sizes continue to decrease.